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Shimpi MT, Sajjad M, Öberg S, Larsson JA. Physical binding energies using the electron localization function in 4-hydroxyphenylboronic acid co-crystals with aza donors. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2023; 35:505901. [PMID: 37659400 DOI: 10.1088/1361-648x/acf638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 09/01/2023] [Indexed: 09/04/2023]
Abstract
Binding energies are traditionally simulated using cluster models by computation of each synthon for each individual co-crystal former. However, our investigation of the binding strengths using the electron localization function (ELF) reveals that these can be determined directly from the crystal supercell computations. We propose a new modeling protocol for the computation of physical binding energies directly from bulk simulations using ELF analysis. In this work, we establish a correlation between ELF values and binding energies calculated for co-crystals of 4-hydroxyphenylboronic acid (4HPBA) with four different aza donors using density functional theory with varying descriptions of dispersion. Boronic acids are gaining significant interest in the field of crystal engineering, but theoretical studies on their use in materials are still very limited. Here, we present a systematic investigation of the non-covalent interactions in experimentally realized co-crystals. Prior diffraction studies on these complexes have shown the competitive nature between the boronic acid functional group and the para-substituted phenolic group forming heteromeric interactions with aza donors. We determine the stability of the co-crystals by simulating their lattice energies, and the different dispersion descriptions show similar trends in lattice energies and lattice parameters. Our study bolsters the experimental observation of the boronic acid group as a competitive co-crystal former in addition to the well-studied phenolic group. Further research on correlating ELF values for physical binding could potentially transform this approach to a viable alternative for the computation of binding energies.
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Affiliation(s)
- Mayura Talwelkar Shimpi
- Applied Physics, Division of Materials Science, Department of Engineering Sciences and Mathematics, Luleå University of Technology, SE-97187 Luleå, Sweden
- Department of Pharmaceutical Biosciences, Uppsala University, PO Box 591, 75124 Uppsala, Sweden
| | - Muhammad Sajjad
- Applied Physics, Division of Materials Science, Department of Engineering Sciences and Mathematics, Luleå University of Technology, SE-97187 Luleå, Sweden
- Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, University of Nottingham Ningbo China, Ningbo, People's Republic of China
| | - Sven Öberg
- Applied Physics, Division of Materials Science, Department of Engineering Sciences and Mathematics, Luleå University of Technology, SE-97187 Luleå, Sweden
| | - J Andreas Larsson
- Applied Physics, Division of Materials Science, Department of Engineering Sciences and Mathematics, Luleå University of Technology, SE-97187 Luleå, Sweden
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2
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El Alouani Dahmouni N, Switlicka A, Machura B, Moliner N, Rabelo R, Ruiz-García R, Stiriba SE, Cano J, Julve M. Bulky countercation effects on the crystal packing of anionic dithiooxalato-containing Ni( ii), Pd( ii) and Pt( ii) complexes: spectroscopic–redox correlations. CrystEngComm 2022. [DOI: 10.1039/d2ce00489e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The metal ion, countercation and crystallization solvent control the packing of bis(dithiooxalato-k2S,S′)metallate(ii) complex anions in the solid state.
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Affiliation(s)
- Nadia El Alouani Dahmouni
- Departament de Química Inorgànica/Instituto de Ciencia Molecular (ICMol), Facultat de Química de la Universitat de València, C/ Catedrático José Beltrán 2, 46980 Paterna, València, Spain
| | - Anna Switlicka
- Department of Crystallography, Institute of Chemistry, University of Silesia, 9th Szkolna St., 40-006 Katowice, Poland
| | - Barbara Machura
- Department of Crystallography, Institute of Chemistry, University of Silesia, 9th Szkolna St., 40-006 Katowice, Poland
| | - Nicolás Moliner
- Departament de Química Inorgànica/Instituto de Ciencia Molecular (ICMol), Facultat de Química de la Universitat de València, C/ Catedrático José Beltrán 2, 46980 Paterna, València, Spain
| | - Renato Rabelo
- Departament de Química Inorgànica/Instituto de Ciencia Molecular (ICMol), Facultat de Química de la Universitat de València, C/ Catedrático José Beltrán 2, 46980 Paterna, València, Spain
| | - Rafael Ruiz-García
- Departament de Química Inorgànica/Instituto de Ciencia Molecular (ICMol), Facultat de Química de la Universitat de València, C/ Catedrático José Beltrán 2, 46980 Paterna, València, Spain
| | - Salah-Eddine Stiriba
- Departament de Química Inorgànica/Instituto de Ciencia Molecular (ICMol), Facultat de Química de la Universitat de València, C/ Catedrático José Beltrán 2, 46980 Paterna, València, Spain
| | - Joan Cano
- Departament de Química Inorgànica/Instituto de Ciencia Molecular (ICMol), Facultat de Química de la Universitat de València, C/ Catedrático José Beltrán 2, 46980 Paterna, València, Spain
| | - Miguel Julve
- Departament de Química Inorgànica/Instituto de Ciencia Molecular (ICMol), Facultat de Química de la Universitat de València, C/ Catedrático José Beltrán 2, 46980 Paterna, València, Spain
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3
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Üstündağ FD, Ünal İ, Cansız D, Üstündağ ÜV, Subaşat HK, Alturfan AA, Tiber PM, Emekli-Alturfan E. 3-Pyridinylboronic acid normalizes the effects of 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine exposure in zebrafish embryos. Drug Chem Toxicol 2020; 45:947-954. [PMID: 32693643 DOI: 10.1080/01480545.2020.1795189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) is a neurotoxin that damages dopaminergic neurons. Zebrafish has been shown to be a suitable model organism to investigate the molecular pathways in the pathogenesis of Parkinson's disease and also for potential therapeutic agent research. Boron has been shown to play an important role in the neural activity of the brain. Boronic acids are used in combinatorial approaches in drug design and discovery. The effect of 3-pyridinylboronic acid which is an important sub-class of heterocyclic boronic acids has not been evaluated in case of MPTP exposure in zebrafish embryos. Accordingly, this study was designed to investigate the effects of 3-pyridinylboronic acid on MPTP exposed zebrafish embryos focusing on the molecular pathways related to neurodegeneration and apoptosis by RT-PCR. Zebrafish embryos were exposed to MPTP (800 μM); MPTP + Low Dose 3-Pyridinylboronic acid (50 μM) (MPTP + LB) and MPTP + High Dose 3-Pyridinylboronic acid (100 μM) (MPTP + HB) in well plates for 72 hours post fertilization. Results of our study showed that MPTP induced a P53 dependent and Bax mediated apoptosis in zebrafish embryos and 3-pyridinylboronic acid restored the locomotor activity and gene expressions related to mitochondrial dysfunction and oxidative stress due to the deleterious effects of MPTP, in a dose-dependent manner.
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Affiliation(s)
- Fümet Duygu Üstündağ
- Faculty of Medicine, Department of Biophysics, Marmara University, Istanbul, Turkey
| | - İsmail Ünal
- Faculty of Dentistry, Department of Basic Medical Sciences, Marmara University, Istanbul, Turkey
| | - Derya Cansız
- Faculty of Medicine, Department of Biochemistry, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Ünsal Veli Üstündağ
- Faculty of Medicine, Medical Biochemistry, Department Medipol University, Istanbul, Turkey
| | - Hülya Kara Subaşat
- Graduate School of Natural and Applied Sciences, Department of Energy, Mugla Sıtkı Kocman University, Muğla, Turkey
| | - A Ata Alturfan
- Faculty of Medicine, Department of Biochemistry, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Pınar Mega Tiber
- Faculty of Medicine, Department of Biophysics, Marmara University, Istanbul, Turkey
| | - Ebru Emekli-Alturfan
- Faculty of Dentistry, Department of Basic Medical Sciences, Marmara University, Istanbul, Turkey
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4
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Ruelas‐Alvarez GY, Cárdenas‐Valenzuela AJ, Cruz‐Enríquez A, Höpfl H, Campos‐Gaxiola JJ, Rodríguez‐Rivera MA, Rodríguez‐Molina B. Exploration of the Luminescence Properties of Organic Phosphate Salts of 3‐Quinoline‐ and 5‐Isoquinolineboronic Acid. Eur J Inorg Chem 2019. [DOI: 10.1002/ejic.201900244] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Glenda Y. Ruelas‐Alvarez
- Facultad de Ingeniería Mochis Universidad Autónoma de Sinaloa Fuente de Poseidón y Prol. A. Flores S/N C.P. 81223 C.U. Los Mochis, Sinaloa México
| | - A. Jaquelin Cárdenas‐Valenzuela
- Facultad de Ingeniería Mochis Universidad Autónoma de Sinaloa Fuente de Poseidón y Prol. A. Flores S/N C.P. 81223 C.U. Los Mochis, Sinaloa México
| | - Adriana Cruz‐Enríquez
- Facultad de Ingeniería Mochis Universidad Autónoma de Sinaloa Fuente de Poseidón y Prol. A. Flores S/N C.P. 81223 C.U. Los Mochis, Sinaloa México
| | - Herbert Höpfl
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas Universidad Autónoma del Estado de Morelos Av. Universidad 1001, C.P. 62209 Cuernavaca México
| | - José J. Campos‐Gaxiola
- Facultad de Ingeniería Mochis Universidad Autónoma de Sinaloa Fuente de Poseidón y Prol. A. Flores S/N C.P. 81223 C.U. Los Mochis, Sinaloa México
| | - Mario A. Rodríguez‐Rivera
- Centro de Investigaciones en Óptica A.C. (CIO) Loma del Bosque #115, Col. Lomas del Campestre, C.P. 37150 León Guanajuato México
| | - Braulio Rodríguez‐Molina
- Instituto de Química Universidad Nacional Autónoma de México Ciudad Universitaria, Del. Coyoacán Ciudad de México México
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5
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Fornasari L, d'Agostino S, Braga D. Zwitterionic Systems Obtained by Condensation of Heteroaryl-Boronic Acids and Rhodizonic Acid. European J Org Chem 2019. [DOI: 10.1002/ejoc.201801754] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Luca Fornasari
- Dipartimento di Chimica G. Ciamician; Università di Bologna; Via Selmi, 2 40126 Bologna Italy
| | - Simone d'Agostino
- Dipartimento di Chimica G. Ciamician; Università di Bologna; Via Selmi, 2 40126 Bologna Italy
| | - Dario Braga
- Dipartimento di Chimica G. Ciamician; Università di Bologna; Via Selmi, 2 40126 Bologna Italy
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6
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Fornasari L, d'Agostino S, Braga D. Supramolecular zwitterions based on a novel boronic acid–squarate dianion synthon. CrystEngComm 2019. [DOI: 10.1039/c9ce00367c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We report a novel heterodimeric charge-assisted hydrogen bonding synthon and prove its robustness by preparation of a three-component co-crystal.
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Affiliation(s)
- Luca Fornasari
- Dipartimento di Chimica G. Ciamician
- Università di Bologna
- 40126 Bologna
- Italy
| | - Simone d'Agostino
- Dipartimento di Chimica G. Ciamician
- Università di Bologna
- 40126 Bologna
- Italy
| | - Dario Braga
- Dipartimento di Chimica G. Ciamician
- Università di Bologna
- 40126 Bologna
- Italy
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7
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Vella-Zarb L, Baisch U. Melaminium Lanthanide Oxalate Coordination Compounds -Synthesis and Structural Varieties. Z Anorg Allg Chem 2017. [DOI: 10.1002/zaac.201700299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Liana Vella-Zarb
- Department of Chemistry; University of Malta; MSD 2080 Msida Malta
- Chemistry; School of Natural & Environmental Sciences; Newcastle University; NE1 7RU Newcastle upon Tyne United Kingdom
| | - Ulrich Baisch
- Department of Chemistry; University of Malta; MSD 2080 Msida Malta
- Chemistry; School of Natural & Environmental Sciences; Newcastle University; NE1 7RU Newcastle upon Tyne United Kingdom
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8
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Campos-Gaxiola JJ, García-Grajeda BA, Hernández-Ahuactzi IF, Guerrero-Álvarez JA, Höpfl H, Cruz-Enríquez A. Supramolecular networks in molecular complexes of pyridine boronic acids and polycarboxylic acids: synthesis, structural characterization and fluorescence properties. CrystEngComm 2017. [DOI: 10.1039/c7ce00762k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
3- and 4-pyridineboronic acids have been combined with trimesic and pyromellitic acids to give three molecular complexes.
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Affiliation(s)
| | | | | | - Jorge A. Guerrero-Álvarez
- Centro de Investigaciones Químicas
- Instituto de Investigación en Ciencias Básicas y Aplicadas
- Universidad Autónoma del Estado de Morelos
- Cuernavaca
- Mexico
| | - Herbert Höpfl
- Centro de Investigaciones Químicas
- Instituto de Investigación en Ciencias Básicas y Aplicadas
- Universidad Autónoma del Estado de Morelos
- Cuernavaca
- Mexico
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9
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Cruz‐Huerta J, Campillo‐Alvarado G, Höpfl H, Rodríguez‐Cuamatzi P, Reyes‐Márquez V, Guerrero‐Álvarez J, Salazar‐Mendoza D, Farfán‐García N. Self‐Assembly of Triphenylboroxine and the Phenylboronic Ester of Pentaerythritol with Piperazine,
trans
‐1,4‐Diaminocyclohexane, and 4‐Aminopyridine. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201501121] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Jorge Cruz‐Huerta
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas e Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Chamilpa, Cuernavaca 62209, Morelos, México
| | - Gonzalo Campillo‐Alvarado
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas e Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Chamilpa, Cuernavaca 62209, Morelos, México
| | - Herbert Höpfl
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas e Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Chamilpa, Cuernavaca 62209, Morelos, México
| | - Patricia Rodríguez‐Cuamatzi
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas e Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Chamilpa, Cuernavaca 62209, Morelos, México
| | - Viviana Reyes‐Márquez
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas e Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Chamilpa, Cuernavaca 62209, Morelos, México
| | - Jorge Guerrero‐Álvarez
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas e Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Chamilpa, Cuernavaca 62209, Morelos, México
| | - Domingo Salazar‐Mendoza
- Universidad Tecnológica de la Mixteca, Carretera a Acatlima Km 2.5, Huajuapan de León 69000, Oaxaca, México
| | - Norberto Farfán‐García
- Facultad de Química, Departamento Química Orgánica, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, México 04510, México
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10
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Hernández-Paredes J, Olvera-Tapia AL, Arenas-García JI, Höpfl H, Morales-Rojas H, Herrera-Ruiz D, Gonzaga-Morales AI, Rodríguez-Fragoso L. On molecular complexes derived from amino acids and nicotinamides in combination with boronic acids. CrystEngComm 2015. [DOI: 10.1039/c4ce01934b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Singh UP, Narang S. A supramolecular approach towards the construction of molecular salts using phosphonic acid and pyrazole. CrystEngComm 2014. [DOI: 10.1039/c4ce00484a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Safa MA, Abo-Amer A, Borecki A, Cooper BFT, Puddephatt RJ. Synthesis and Self-Association of Organoplatinum(IV) Boronic Acids. Organometallics 2012. [DOI: 10.1021/om2009217] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Muhieddine A. Safa
- Department
of Chemistry, University of Western Ontario, London, Canada N6A 5B7
| | - Anwar Abo-Amer
- Department
of Chemistry, University of Western Ontario, London, Canada N6A 5B7
- Department
of Chemistry, Al al-Bayt University, Al-Mafraq, Jordan
| | - Aneta Borecki
- Department
of Chemistry, University of Western Ontario, London, Canada N6A 5B7
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13
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Kara H, Adams CJ, Schwarz B, Orpen AG. The use of [Fe(dithiooxalate)2(NO)]2− as a tecton in crystal engineering. CrystEngComm 2011. [DOI: 10.1039/c1ce05309d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Vega A, Luna R, Tlahuext H, Höpfl H. Bis[3-(dihydroxy-boryl)anilinium] sulfate. Acta Crystallogr Sect E Struct Rep Online 2010; 66:o1035-6. [PMID: 21579098 PMCID: PMC2979015 DOI: 10.1107/s1600536810012092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 03/30/2010] [Indexed: 05/26/2023]
Abstract
In the title compound, 2C6H9BNO2+·SO42−, the dihydroxyboryl group of one of the two independent boronic acid molecules participates in (B)O—H⋯OB and N—H⋯OB hydrogen bonds, while the second is involved mainly in the formation of the charge-assisted heterodimeric synthon –B(OH)2⋯−O2SO2−. These aggregates are further connected through N—H⋯Osulfate interactions, forming a complex three-dimensional hydrogen-bonded network.
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Affiliation(s)
- Araceli Vega
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, CP 62209, Cuernavaca, Mexico
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15
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Vega A, Zarate M, Tlahuext H, Höpfl H. Benzene-1,4-diboronic acid-4,4'-bipyridine-water (1/2/2). Acta Crystallogr C 2010; 66:o219-21. [PMID: 20354315 DOI: 10.1107/s0108270110009121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Accepted: 03/10/2010] [Indexed: 11/10/2022] Open
Abstract
In the presence of water, benzene-1,4-diboronic acid (1,4-bdba) and 4,4'-bipyridine (4,4'-bpy) form a cocrystal of composition (1,4-bdba)(4,4'-bpy)(2)(H(2)O)(2), in which the molecular components are organized in two, so far unknown, cyclophane-type hydrogen-bonding patterns. The asymmetric unit of the title compound, C(6)H(8)B(2)O(4).2C(10)H(8)N(2).2H(2)O, contains two 4,4'-bpy, two water molecules and two halves of 1,4-bdba molecules arranged around crystallographic inversion centers. The occurrence of O-H...O and O-H...N hydrogen bonds involving the water molecules and all O atoms of boronic acid gives rise to a two-dimensional hydrogen-bonded layer structure that develops parallel to the (01-4) plane. This supramolecular organization is reinforced by pi-pi interactions between symmetry-related 4,4'-bpy molecules.
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Affiliation(s)
- Araceli Vega
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, CP 62209, Cuernavaca, Mexico
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16
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Baisch U, Braga D. [Yb(C2O4)4]5−– a versatile metal–organic building block for layered coordination polymers. CrystEngComm 2009. [DOI: 10.1039/b816022h] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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